Multiple sequence alignment - TraesCS5A01G174100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G174100 chr5A 100.000 4443 0 0 1 4443 367268817 367273259 0.000000e+00 8205
1 TraesCS5A01G174100 chr5A 75.172 2324 530 33 1019 3314 477222146 477224450 0.000000e+00 1051
2 TraesCS5A01G174100 chr5D 97.467 4225 85 7 1 4220 278136555 278140762 0.000000e+00 7190
3 TraesCS5A01G174100 chr5D 75.086 2324 532 33 1019 3314 376178455 376180759 0.000000e+00 1040
4 TraesCS5A01G174100 chr5B 96.742 3591 100 11 657 4234 316151774 316155360 0.000000e+00 5967
5 TraesCS5A01G174100 chr5B 75.172 2324 530 33 1019 3314 449129950 449132254 0.000000e+00 1051
6 TraesCS5A01G174100 chr5B 91.247 457 24 6 1 448 316150779 316151228 3.800000e-170 608
7 TraesCS5A01G174100 chr5B 83.249 591 34 20 3875 4443 316155357 316155904 2.400000e-132 483
8 TraesCS5A01G174100 chr5B 91.061 179 12 3 442 617 316151590 316151767 5.740000e-59 239


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G174100 chr5A 367268817 367273259 4442 False 8205.00 8205 100.00000 1 4443 1 chr5A.!!$F1 4442
1 TraesCS5A01G174100 chr5A 477222146 477224450 2304 False 1051.00 1051 75.17200 1019 3314 1 chr5A.!!$F2 2295
2 TraesCS5A01G174100 chr5D 278136555 278140762 4207 False 7190.00 7190 97.46700 1 4220 1 chr5D.!!$F1 4219
3 TraesCS5A01G174100 chr5D 376178455 376180759 2304 False 1040.00 1040 75.08600 1019 3314 1 chr5D.!!$F2 2295
4 TraesCS5A01G174100 chr5B 316150779 316155904 5125 False 1824.25 5967 90.57475 1 4443 4 chr5B.!!$F2 4442
5 TraesCS5A01G174100 chr5B 449129950 449132254 2304 False 1051.00 1051 75.17200 1019 3314 1 chr5B.!!$F1 2295

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
247 255 1.281899 CGAGATTTGAGGCGAGGAAC 58.718 55.000 0.00 0.0 0.00 3.62 F
1160 1559 0.955919 GTCAAGGCCAAAGACCTCCG 60.956 60.000 5.01 0.0 36.14 4.63 F
1270 1669 1.072648 CTAACCCGGAGTGGAACCAAA 59.927 52.381 0.73 0.0 42.00 3.28 F
2049 2471 2.134287 TAGCGATCTGAGGGCCACC 61.134 63.158 6.18 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 2340 0.399949 TGTTCCCCATCTCCCGCTAT 60.400 55.000 0.00 0.00 0.00 2.97 R
2049 2471 0.514691 GCTTCCACAGCTGTTTCTCG 59.485 55.000 18.94 5.27 46.27 4.04 R
3183 3608 1.945522 CACAACCATGCGAAACGGA 59.054 52.632 0.00 0.00 0.00 4.69 R
3583 4008 2.441532 CAGGGCCAGGCAATCAGG 60.442 66.667 15.19 0.00 0.00 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 4.469552 CGTGATTTTAGGGGTTTCGAAAC 58.530 43.478 28.83 28.83 38.17 2.78
81 82 3.628008 AGGGGTTTCGAAACTTCAAAGT 58.372 40.909 33.23 13.59 42.04 2.66
120 128 2.883122 ATGTACGGCCCCTGTTTTTA 57.117 45.000 0.00 0.00 0.00 1.52
121 129 2.883122 TGTACGGCCCCTGTTTTTAT 57.117 45.000 0.00 0.00 0.00 1.40
122 130 3.157750 TGTACGGCCCCTGTTTTTATT 57.842 42.857 0.00 0.00 0.00 1.40
123 131 3.498334 TGTACGGCCCCTGTTTTTATTT 58.502 40.909 0.00 0.00 0.00 1.40
124 132 3.896272 TGTACGGCCCCTGTTTTTATTTT 59.104 39.130 0.00 0.00 0.00 1.82
125 133 5.075493 TGTACGGCCCCTGTTTTTATTTTA 58.925 37.500 0.00 0.00 0.00 1.52
126 134 5.715753 TGTACGGCCCCTGTTTTTATTTTAT 59.284 36.000 0.00 0.00 0.00 1.40
127 135 5.748670 ACGGCCCCTGTTTTTATTTTATT 57.251 34.783 0.00 0.00 0.00 1.40
128 136 6.116711 ACGGCCCCTGTTTTTATTTTATTT 57.883 33.333 0.00 0.00 0.00 1.40
129 137 6.535540 ACGGCCCCTGTTTTTATTTTATTTT 58.464 32.000 0.00 0.00 0.00 1.82
130 138 6.999272 ACGGCCCCTGTTTTTATTTTATTTTT 59.001 30.769 0.00 0.00 0.00 1.94
174 182 2.418976 GGGTTGCTAGGAAACGATGAAC 59.581 50.000 5.89 0.00 0.00 3.18
212 220 6.097915 TGTTGTTGTGTTTTTCCTTTACCA 57.902 33.333 0.00 0.00 0.00 3.25
247 255 1.281899 CGAGATTTGAGGCGAGGAAC 58.718 55.000 0.00 0.00 0.00 3.62
375 392 8.741603 TGTTTTTATTATTAGTGGGCTACTCC 57.258 34.615 6.84 0.00 40.89 3.85
624 1016 3.074412 AGCATTACCTGTTACACACTGC 58.926 45.455 0.00 0.00 0.00 4.40
976 1375 2.985957 ATTTTGTTGCAGGCACAAGT 57.014 40.000 2.91 0.00 0.00 3.16
1054 1453 2.169769 TCGTTGAAAGAGACAACACCCT 59.830 45.455 0.00 0.00 45.09 4.34
1160 1559 0.955919 GTCAAGGCCAAAGACCTCCG 60.956 60.000 5.01 0.00 36.14 4.63
1194 1593 3.403624 GGGAGCTGTGACCCATCA 58.596 61.111 3.30 0.00 44.96 3.07
1270 1669 1.072648 CTAACCCGGAGTGGAACCAAA 59.927 52.381 0.73 0.00 42.00 3.28
1794 2216 3.003480 GGAGCACTTGATTCTTAGCGTT 58.997 45.455 0.00 0.00 0.00 4.84
1918 2340 5.428253 GGTGGTGTAATCTTGAGAAGCATA 58.572 41.667 0.00 0.00 0.00 3.14
2049 2471 2.134287 TAGCGATCTGAGGGCCACC 61.134 63.158 6.18 0.00 0.00 4.61
2140 2562 3.117888 GGCAATGAAGACTAAGGATGGGA 60.118 47.826 0.00 0.00 0.00 4.37
2630 3055 3.695606 TGCCGAGCCACCTCTCAC 61.696 66.667 0.00 0.00 35.90 3.51
2723 3148 7.913674 ACTTCTTCAGGATTATGAAAGTGTC 57.086 36.000 0.00 0.00 38.66 3.67
2825 3250 6.817765 TCTCCTGTTCATCATTTTGGTTAC 57.182 37.500 0.00 0.00 0.00 2.50
2863 3288 2.142356 TCCGACCGTTTCCCTGTATA 57.858 50.000 0.00 0.00 0.00 1.47
2988 3413 4.569719 TGAGGAGTTTGATACTTTCCCC 57.430 45.455 0.00 0.00 37.17 4.81
3244 3669 4.115199 GGCATCCCAGGTTCCGCT 62.115 66.667 0.00 0.00 0.00 5.52
3656 4083 9.851686 TTCTCCTAAAATATGTTGCATATCTGT 57.148 29.630 2.57 0.00 0.00 3.41
3673 4100 4.233632 TCTGTGGTATGATTTGCATCCA 57.766 40.909 0.00 0.00 38.44 3.41
3697 4124 6.521151 AAAATGGAATCAGTGGTGAGATTC 57.479 37.500 6.61 6.61 45.84 2.52
3753 4180 4.893608 TGCTTTTTCAGATAAAAAGGCCC 58.106 39.130 19.16 7.97 45.44 5.80
3803 4230 3.316308 ACCATTGACAAAACTGCTCTCAC 59.684 43.478 0.00 0.00 0.00 3.51
3805 4232 2.595124 TGACAAAACTGCTCTCACGA 57.405 45.000 0.00 0.00 0.00 4.35
3841 4268 8.512138 AGTGCCTGTACTTGTATTTCAATAAAC 58.488 33.333 0.00 0.00 35.35 2.01
3864 4291 5.694006 ACTAGCGTCAAGATCAGAATTATGC 59.306 40.000 0.00 0.00 0.00 3.14
4019 4446 2.691409 ATACACGGGTCCAGAACATG 57.309 50.000 0.00 0.00 0.00 3.21
4220 4652 1.920610 ACCTACACGTAGTTGGAGCT 58.079 50.000 19.30 0.00 44.69 4.09
4234 4666 3.411703 GAGCTTGCGCGATCACACG 62.412 63.158 12.10 0.00 42.32 4.49
4276 5033 1.029947 GCCGCCTTTGCCTAAAGCTA 61.030 55.000 0.00 0.00 41.55 3.32
4277 5034 1.459450 CCGCCTTTGCCTAAAGCTAA 58.541 50.000 0.00 0.00 41.55 3.09
4278 5035 1.816224 CCGCCTTTGCCTAAAGCTAAA 59.184 47.619 0.00 0.00 41.55 1.85
4279 5036 2.230266 CCGCCTTTGCCTAAAGCTAAAA 59.770 45.455 0.00 0.00 41.55 1.52
4280 5037 3.242518 CGCCTTTGCCTAAAGCTAAAAC 58.757 45.455 0.00 0.00 41.55 2.43
4281 5038 3.242518 GCCTTTGCCTAAAGCTAAAACG 58.757 45.455 0.00 0.00 41.55 3.60
4282 5039 3.305131 GCCTTTGCCTAAAGCTAAAACGT 60.305 43.478 0.00 0.00 41.55 3.99
4283 5040 4.226761 CCTTTGCCTAAAGCTAAAACGTG 58.773 43.478 0.00 0.00 41.55 4.49
4284 5041 4.261447 CCTTTGCCTAAAGCTAAAACGTGT 60.261 41.667 0.00 0.00 41.55 4.49
4285 5042 4.904253 TTGCCTAAAGCTAAAACGTGTT 57.096 36.364 0.00 0.00 44.23 3.32
4286 5043 4.477302 TGCCTAAAGCTAAAACGTGTTC 57.523 40.909 0.00 0.00 44.23 3.18
4287 5044 3.878103 TGCCTAAAGCTAAAACGTGTTCA 59.122 39.130 0.00 0.00 44.23 3.18
4312 5069 1.615392 GAAGCAAAGTGTTGGAGCCAT 59.385 47.619 0.00 0.00 35.10 4.40
4339 5096 1.745653 TGCACTCACTCGGTCTATCTG 59.254 52.381 0.00 0.00 0.00 2.90
4340 5097 1.535015 GCACTCACTCGGTCTATCTGC 60.535 57.143 0.00 0.00 0.00 4.26
4342 5099 1.064314 ACTCACTCGGTCTATCTGCCT 60.064 52.381 0.00 0.00 0.00 4.75
4343 5100 2.028130 CTCACTCGGTCTATCTGCCTT 58.972 52.381 0.00 0.00 0.00 4.35
4372 5148 1.213926 CCCTTGAAGAGCATAGGCCTT 59.786 52.381 12.58 0.00 42.56 4.35
4436 5213 2.333926 GTGGCGCCAAAACTTTAATCC 58.666 47.619 34.66 10.48 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 2.289547 CAGGGGCCGTACATAAAATTCG 59.710 50.000 0.00 0.00 0.00 3.34
128 136 3.500680 GGACGTAAGCACCATCTCAAAAA 59.499 43.478 0.00 0.00 45.62 1.94
129 137 3.071479 GGACGTAAGCACCATCTCAAAA 58.929 45.455 0.00 0.00 45.62 2.44
130 138 2.614481 GGGACGTAAGCACCATCTCAAA 60.614 50.000 0.00 0.00 45.62 2.69
199 207 9.384764 CTTTTGGTGTTTATGGTAAAGGAAAAA 57.615 29.630 0.00 0.00 0.00 1.94
212 220 5.705609 AATCTCGTGCTTTTGGTGTTTAT 57.294 34.783 0.00 0.00 0.00 1.40
247 255 5.715429 CAGAGTAACTGCTGCTAAATCTG 57.285 43.478 0.00 4.46 39.86 2.90
360 377 1.120530 CACCGGAGTAGCCCACTAAT 58.879 55.000 9.46 0.00 37.72 1.73
361 378 0.040058 TCACCGGAGTAGCCCACTAA 59.960 55.000 9.46 0.00 37.72 2.24
362 379 0.682209 GTCACCGGAGTAGCCCACTA 60.682 60.000 9.46 0.00 37.72 2.74
375 392 1.068541 TCAGTCATTCACTCGTCACCG 60.069 52.381 0.00 0.00 30.26 4.94
406 423 3.347216 GCATTGGTATTGTCACTGACCT 58.653 45.455 6.72 0.00 32.87 3.85
624 1016 6.365247 GCATCTACGTGTAACAGGTAATATGG 59.635 42.308 0.00 0.00 34.94 2.74
840 1235 7.490000 TGCATGTCATGTGCATAATCAAATAA 58.510 30.769 14.26 0.00 46.76 1.40
919 1318 4.783764 TCAAGAAGAGCTTCACGTATGA 57.216 40.909 12.32 6.00 41.84 2.15
976 1375 0.679505 CCGGTTCACAGAAGGTCAGA 59.320 55.000 0.00 0.00 0.00 3.27
1054 1453 0.907230 GCCATAAAACCCCCAAGGCA 60.907 55.000 0.00 0.00 40.58 4.75
1160 1559 1.379044 CCAGACCCATCCTTGGCAC 60.379 63.158 0.00 0.00 42.15 5.01
1194 1593 5.707066 AATTCCCAAGCTTGATCTCTACT 57.293 39.130 28.05 1.53 0.00 2.57
1270 1669 2.999185 TCCTTGGGAAAGGCAAAGAT 57.001 45.000 0.00 0.00 39.80 2.40
1291 1690 4.492646 TCAATATAGGAGGACTGGATGCA 58.507 43.478 0.00 0.00 0.00 3.96
1367 1778 3.181454 TGGGACTCTCTTTGGAACTTCAC 60.181 47.826 0.00 0.00 0.00 3.18
1794 2216 2.108976 GGCGCAATCCGATCCTCA 59.891 61.111 10.83 0.00 40.02 3.86
1918 2340 0.399949 TGTTCCCCATCTCCCGCTAT 60.400 55.000 0.00 0.00 0.00 2.97
2049 2471 0.514691 GCTTCCACAGCTGTTTCTCG 59.485 55.000 18.94 5.27 46.27 4.04
2140 2562 4.012374 CAGTAAGAATCTGTGGTGCCATT 58.988 43.478 0.00 0.00 0.00 3.16
2630 3055 6.287107 ACATGTACTCAACAACTTCTTTCG 57.713 37.500 0.00 0.00 42.70 3.46
2825 3250 2.275318 GAAGGATCAGCTCTGGAAACG 58.725 52.381 0.00 0.00 0.00 3.60
2863 3288 2.379907 ACCAGACCCCAATCAAGAACAT 59.620 45.455 0.00 0.00 0.00 2.71
3183 3608 1.945522 CACAACCATGCGAAACGGA 59.054 52.632 0.00 0.00 0.00 4.69
3333 3758 4.713553 TGCTGGAAAACACTCTGATGTTA 58.286 39.130 6.09 0.00 42.01 2.41
3583 4008 2.441532 CAGGGCCAGGCAATCAGG 60.442 66.667 15.19 0.00 0.00 3.86
3641 4066 8.785946 CAAATCATACCACAGATATGCAACATA 58.214 33.333 0.00 0.00 31.26 2.29
3655 4082 6.037391 CCATTTTTGGATGCAAATCATACCAC 59.963 38.462 13.51 0.00 35.02 4.16
3656 4083 6.070366 TCCATTTTTGGATGCAAATCATACCA 60.070 34.615 13.51 0.00 35.02 3.25
3673 4100 6.349611 CGAATCTCACCACTGATTCCATTTTT 60.350 38.462 9.27 0.00 43.13 1.94
3697 4124 3.371898 TCAATGCTTCACATGCTAAGACG 59.628 43.478 10.91 0.00 39.60 4.18
3753 4180 5.215252 TCTAGACCTCAACAAAGTCTTGG 57.785 43.478 0.00 0.00 41.09 3.61
3803 4230 5.833082 AGTACAGGCACTATAACTCAATCG 58.167 41.667 0.00 0.00 36.02 3.34
3805 4232 6.947464 ACAAGTACAGGCACTATAACTCAAT 58.053 36.000 0.00 0.00 36.02 2.57
3841 4268 5.164109 CGCATAATTCTGATCTTGACGCTAG 60.164 44.000 0.00 0.00 0.00 3.42
3864 4291 5.753438 ACTACATATATGTGTTGCTTCCACG 59.247 40.000 25.48 2.73 41.89 4.94
4141 4568 0.858961 CGCTTTAGTTGCGCTGATGC 60.859 55.000 9.73 3.13 46.72 3.91
4248 5005 1.299773 CAAAGGCGGCGCAAAAGAA 60.300 52.632 34.36 0.00 0.00 2.52
4249 5006 2.334653 CAAAGGCGGCGCAAAAGA 59.665 55.556 34.36 0.00 0.00 2.52
4251 5008 4.959596 GGCAAAGGCGGCGCAAAA 62.960 61.111 34.36 0.00 42.47 2.44
4276 5033 1.065551 GCTTCAGCCTGAACACGTTTT 59.934 47.619 2.24 0.00 32.21 2.43
4277 5034 0.663153 GCTTCAGCCTGAACACGTTT 59.337 50.000 2.24 0.00 32.21 3.60
4278 5035 0.463654 TGCTTCAGCCTGAACACGTT 60.464 50.000 2.24 0.00 41.18 3.99
4279 5036 0.463654 TTGCTTCAGCCTGAACACGT 60.464 50.000 2.24 0.00 41.18 4.49
4280 5037 0.662619 TTTGCTTCAGCCTGAACACG 59.337 50.000 2.24 0.00 41.18 4.49
4281 5038 1.678101 ACTTTGCTTCAGCCTGAACAC 59.322 47.619 2.24 0.00 41.18 3.32
4282 5039 1.677576 CACTTTGCTTCAGCCTGAACA 59.322 47.619 2.24 4.48 41.18 3.18
4283 5040 1.678101 ACACTTTGCTTCAGCCTGAAC 59.322 47.619 2.24 1.83 41.18 3.18
4284 5041 2.057137 ACACTTTGCTTCAGCCTGAA 57.943 45.000 7.00 7.00 41.18 3.02
4285 5042 1.677576 CAACACTTTGCTTCAGCCTGA 59.322 47.619 0.00 0.00 41.18 3.86
4286 5043 1.269413 CCAACACTTTGCTTCAGCCTG 60.269 52.381 0.00 0.00 41.18 4.85
4287 5044 1.035139 CCAACACTTTGCTTCAGCCT 58.965 50.000 0.00 0.00 41.18 4.58
4312 5069 1.591703 CGAGTGAGTGCAGGCCTTA 59.408 57.895 0.00 0.00 0.00 2.69
4326 5083 2.952978 CAGTAAGGCAGATAGACCGAGT 59.047 50.000 0.00 0.00 0.00 4.18
4339 5096 1.745489 CAAGGGCGTCCAGTAAGGC 60.745 63.158 9.71 0.00 37.29 4.35
4340 5097 0.323629 TTCAAGGGCGTCCAGTAAGG 59.676 55.000 9.71 0.00 39.47 2.69
4342 5099 1.275291 CTCTTCAAGGGCGTCCAGTAA 59.725 52.381 9.71 0.00 34.83 2.24
4343 5100 0.895530 CTCTTCAAGGGCGTCCAGTA 59.104 55.000 9.71 0.00 34.83 2.74
4398 5175 1.520120 CCACTCGCGAGCATGATGT 60.520 57.895 34.83 12.74 0.00 3.06
4399 5176 1.520120 ACCACTCGCGAGCATGATG 60.520 57.895 34.83 23.92 0.00 3.07
4400 5177 1.520120 CACCACTCGCGAGCATGAT 60.520 57.895 34.83 12.28 0.00 2.45
4401 5178 2.125952 CACCACTCGCGAGCATGA 60.126 61.111 34.83 0.00 0.00 3.07
4402 5179 3.190849 CCACCACTCGCGAGCATG 61.191 66.667 34.83 27.22 0.00 4.06


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.